Blythe will be setting up a comms consultancy later in the year and is to be replaced by adviser to the governor Jenny Scott, who returns to the role she left in 2011.
He said: "I have hugely enjoyed working at the Bank of England for the past three years. In that time the Communications Directorate has expanded to match the Bank’s wide-ranging new responsibilities and has played a key role in the transition to new leadership of the organisation.
"It has been a pleasure to work with such talented and dedicated colleagues at the Bank. I am now looking forward to a long summer break, setting up my own communications consultancy in the autumn and a continued association with the Bank of England."
Blythe will leave in mid-July and take a career break while continuing to act as a consultant to the Bank.
He took on the job from Scott, who will not be replaced when she switches jobs, after a two-decade career with the BBC where he played a leading role in covering the financial crisis.
Bank of England governor Mark Carney said: "I am extremely grateful to Nils for his advice and assistance to me during the transition to, and first year of, my term as governor.
"He has made an enormous contribution to the Bank over the past three years and during that period has successfully transformed the Bank’s communications function to serve the Bank’s greatly expanded range of responsibilities and powers. I and my fellow governors wish Nils every success with the next phase of his career.
"I am also grateful that Nils raised this possibility with me some months ago and that Jenny Scott has agreed to succeed him in the post of executive director, communications."
Scott first joined the bank in 1992 as an economist before leaving to take up a career in journalism, which included becoming the BBC's economics correspondent and presenting BBC2’s The Daily Politics with Andrew Neil.
Returning to the bank in July 2008 as executive director, communications, she then left to look after her young family in 2011 before being appointed to advise Carney last June.